Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01014712.1 Kokia drynarioides strain JFW-HI SEQ_129751, whole genome shotgun sequence

Parameters: 2 7 7 80 10 50 1000

Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000

Length: 14211
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33

Warning! 10 characters in sequence are not A, C, G, or T


Found at i:169 original size:16 final size:16

Alignment explanation


    Indices: 123--171  Score: 59
    Period size: 16  Copynumber: 3.2  Consensus size: 16

        113 TAAACCTAAC

                      *     
        123 TAATTAATTACCAAAA
          1 TAATTAATTATCAAAA

                       *    
        139 T-A-TAA-TATAAAAA
          1 TAATTAATTATCAAAA

                            
        152 TAATTAATTATCAAAA
          1 TAATTAATTATCAAAA

                
        168 TAAT
          1 TAAT

        172 ATCCCCATCA


Statistics
Matches: 27,  Mismatches: 3, Indels: 6
        0.75            0.08        0.17

Matches are distributed among these distances:
  13    7  0.26
  14    4  0.15
  15    4  0.15
  16   12  0.44

ACGTcount: A:0.59, C:0.06, G:0.00, T:0.35


Consensus pattern (16 bp):   
TAATTAATTATCAAAA

Found at i:238 original size:30 final size:30

Alignment explanation


    Indices: 204--298  Score: 86
    Period size: 30  Copynumber: 3.2  Consensus size: 30

        194 AAATGGTACA

                      *                   
        204 AAATAAATATTTATTTTGTACCATTTTAGT
          1 AAATAAATATATATTTTGTACCATTTTAGT

                     ** * * *     *     *  
        234 AAAT-AAT-GGTGTGTGGATACTATTTTGGT
          1 AAATAAATATATATTTTG-TACCATTTTAGT

             *                            
        263 ATATAAATATATATTTTGTACCATTTTAGT
          1 AAATAAATATATATTTTGTACCATTTTAGT

                  
        293 AAATAA
          1 AAATAA

        299 CACATTTTGA


Statistics
Matches: 46,  Mismatches: 16, Indels: 6
        0.68            0.24        0.09

Matches are distributed among these distances:
  28    4  0.09
  29   16  0.35
  30   22  0.48
  31    4  0.09

ACGTcount: A:0.37, C:0.05, G:0.13, T:0.45


Consensus pattern (30 bp):   
AAATAAATATATATTTTGTACCATTTTAGT

Found at i:1553 original size:43 final size:43

Alignment explanation


    Indices: 1471--1555  Score: 118
    Period size: 43  Copynumber: 2.0  Consensus size: 43

       1461 ATTAACATGT

                                  *        *           
       1471 TAAATTATATTACTTGACTCGTGTTAATATGGTTGCATGTTAC
          1 TAAATTATATTACTTGACTCGTATTAATATGATTGCATGTTAC

                           *    *                      
       1514 TAAATTATATTACTTTACTCTTATTAATAT-ATTGACATGTTA
          1 TAAATTATATTACTTGACTCGTATTAATATGATTG-CATGTTA

       1556 TTAATTGTGC


Statistics
Matches: 37,  Mismatches: 4, Indels: 2
        0.86            0.09        0.05

Matches are distributed among these distances:
  42    3  0.08
  43   34  0.92

ACGTcount: A:0.32, C:0.11, G:0.11, T:0.47


Consensus pattern (43 bp):   
TAAATTATATTACTTGACTCGTATTAATATGATTGCATGTTAC

Found at i:2257 original size:45 final size:45

Alignment explanation


    Indices: 2122--2250  Score: 204
    Period size: 45  Copynumber: 2.9  Consensus size: 45

       2112 GCATAGCTCA

                *                                        
       2122 TCAATCCAAGGATATCAGCCTCAGTTTGACGAGCCACCGCAATAC
          1 TCAAGCCAAGGATATCAGCCTCAGTTTGACGAGCCACCGCAATAC

                                   *                     
       2167 TCAAGCCAAGGATATCAGCCTCAATTTGACGAGCCACCGCAATAC
          1 TCAAGCCAAGGATATCAGCCTCAGTTTGACGAGCCACCGCAATAC

                 **           *  *                 
       2212 TCAAGGGAAGGATATCAGGCTGAGTTTGACGAGCCACCG
          1 TCAAGCCAAGGATATCAGCCTCAGTTTGACGAGCCACCG

       2251 TGATACTTTA


Statistics
Matches: 77,  Mismatches: 7, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  45   77  1.00

ACGTcount: A:0.31, C:0.28, G:0.22, T:0.19


Consensus pattern (45 bp):   
TCAAGCCAAGGATATCAGCCTCAGTTTGACGAGCCACCGCAATAC

Found at i:2567 original size:28 final size:28

Alignment explanation


    Indices: 2536--2602  Score: 89
    Period size: 28  Copynumber: 2.4  Consensus size: 28

       2526 ACCTAAATTG

                 *                      
       2536 TAAACCCTAGACTTAAAACCCTAAACCA
          1 TAAACACTAGACTTAAAACCCTAAACCA

                    *     *    *       *
       2564 TAAACACTGGACTTGAAACTCTAAACCG
          1 TAAACACTAGACTTAAAACCCTAAACCA

                       
       2592 TAAACACTAGA
          1 TAAACACTAGA

       2603 TTGATTAAGG


Statistics
Matches: 33,  Mismatches: 6, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
  28   33  1.00

ACGTcount: A:0.45, C:0.27, G:0.09, T:0.19


Consensus pattern (28 bp):   
TAAACACTAGACTTAAAACCCTAAACCA

Found at i:12251 original size:32 final size:30

Alignment explanation


    Indices: 12214--12298  Score: 93
    Period size: 32  Copynumber: 2.7  Consensus size: 30

      12204 ATTAGTAATC

                                      *      
      12214 AGTAGTTAGT-TACTGTTAATAAATTTGTTAGT
          1 AGTAGTTAGTCTACTGTT-AT-AA-TGGTTAGT

                        *                 
      12246 AGTAGTTA-TCTTCTGTTATAATGGTTAGT
          1 AGTAGTTAGTCTACTGTTATAATGGTTAGT

                                    
      12275 AGTAGTTAGTCTACTTGTATATAA
          1 AGTAGTTAGTCTAC-TGT-TATAA

      12299 AAGGTTAATA


Statistics
Matches: 46,  Mismatches: 3, Indels: 8
        0.81            0.05        0.14

Matches are distributed among these distances:
  29   15  0.33
  30    6  0.13
  31    6  0.13
  32   19  0.41

ACGTcount: A:0.29, C:0.06, G:0.19, T:0.46


Consensus pattern (30 bp):   
AGTAGTTAGTCTACTGTTATAATGGTTAGT
Done.